Question: problem with bedtools complement: how to extract strand information?
gravatar for biolab
5.8 years ago by
biolab1.2k wrote:

Hi everyone,

I have a minor trouble when using bedtools complement.  My gff3 file contains Chr start end strand ect. information.  I want to use bedtools complement to extract other regions, however, the command  bedtools complement -i gff_file -g genome_file  gives me three columns: Chr, start, end.  The output does not have strand information.

Thank you very much.

bedtools • 2.0k views
ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by biolab1.2k

this tool would give you the regions of your genome_file which are not in your gff_file. what strand you expect from output ?

ADD REPLYlink written 5.8 years ago by Manvendra Singh2.1k
gravatar for iraun
5.8 years ago by
iraun3.8k wrote:

You can not get additional information about the complement regions of your interest regions. The main goal of executing bedtools complement command should be to get all off-target regions of your genome, not to "annotate" those regions.

ADD COMMENTlink written 5.8 years ago by iraun3.8k

Thanks a lot, Manu and airan, i understand the command only outputs region range information.

ADD REPLYlink written 5.8 years ago by biolab1.2k
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